Iva Veseli of anvi'o


Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.


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Intellectual contributions

Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.

Program contributions

anvi-compute-functional-enrichment-across-genomes anvi-compute-functional-enrichment-in-pan anvi-compute-metabolic-enrichment anvi-display-metabolism anvi-estimate-metabolism anvi-migrate anvi-run-hmms anvi-run-kegg-kofams anvi-run-pfams anvi-setup-kegg-data anvi-setup-pfams anvi-setup-user-modules anvi-summarize-blitz anvi-script-estimate-metabolic-independence anvi-script-gen-genomes-file anvi-script-gen-user-module-file

Resource contributions

Tutorials and exercises

Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.

An exercise on metabolic reconstruction in anvi'o A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules.
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
A metagenomics workshop featuring anvi'o Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
Another anvi'o workshop on metagenomics Materials and a tutorial from the 2023 iteration of our metagenomics workshop.

Technical write-ups

Solutions or discussions regarding matters that are typically more technical than scientific.

Getting help from the anvi'o community A resource that describes how to find anvi'o programs and understand their utility, how to reach out to anvi'o community, and how to report technical problems.

Articles, workflows, opinions

Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.

The Ruegeria pomeroyi digital microbe Showcasing our strategy for consolidating and sharing data with a C-CoMP model organism.